Comparison of Oral Collection Methods for Studies of Microbiota

Cancer Epidemiol Biomarkers Prev. 2019 Jan;28(1):137-143. doi: 10.1158/1055-9965.EPI-18-0312. Epub 2018 Sep 27.


Background: A number of cohort studies have collected Scope mouthwash samples by mail, which are being used for microbiota measurements. We evaluated the stability of Scope mouthwash samples at ambient temperature and determined the comparability of Scope mouthwash with saliva collection using the OMNIgene ORAL Kit.

Methods: Fifty-three healthy volunteers from Mayo Clinic and 50 cohort members from Bangladesh provided oral samples. One aliquot of the OMNIgene ORAL and Scope mouthwash were frozen immediately and one aliquot of the Scope mouthwash remained at ambient temperature for 4 days and was then frozen. DNA was extracted and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using the HiSeq. Intraclass correlation coefficients (ICC) were calculated.

Results: The overall stability of the Scope mouthwash samples was relatively high for alpha and beta diversity. For example, the meta-analyzed ICC for the Shannon index was 0.86 (95% confidence interval, 0.76-0.96). Similarly, the ICCs for the relative abundance of the top 25 genera were generally high. The comparability of the two sample types was relatively low when measured using ICCs, but were increased by using a Spearman correlation coefficient (SCC) to compare the rank order of individuals.

Conclusions: Overall, the Scope mouthwash samples appear to be stable at ambient temperature, which suggests that oral rinse samples received by the mail can be used for microbial analyses. However, Scope mouthwash samples were distinct compared with OMNIgene ORAL samples.

Impact: Studies should try to compare oral microbial metrics within one sample collection type.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Bangladesh
  • Cetylpyridinium
  • DNA Barcoding, Taxonomic
  • DNA, Bacterial
  • Drug Combinations
  • Healthy Volunteers
  • Humans
  • Microbiota / genetics*
  • Quaternary Ammonium Compounds
  • RNA, Ribosomal, 16S / analysis
  • RNA, Ribosomal, 16S / genetics*
  • Saliva / microbiology*
  • Specimen Handling / methods*
  • United States


  • DNA, Bacterial
  • Drug Combinations
  • Quaternary Ammonium Compounds
  • RNA, Ribosomal, 16S
  • Scope mouthwash
  • Cetylpyridinium